Error in read.celfile.header(x) : Is GSE30521/CEL/GPL9793_gene_assignments.txt.gz really a CEL file

Question

[muhammadzubair777]

hello Dear! i am analyzing data through R and during analyzing , file read error is coming.

the using code is here. after readcell file there is an error give in box.

source("http://bioconductor.org/biocLite.R")

biocLite("huex10sttranscriptcluster.db")

biocLite("pd.huex.1.0.st.v2")

library(GEOquery)

library(affy)

library(limma)

library(annotate)

library(oligo)

library("pd.huex.1.0.st.v2")

library("huex10sttranscriptcluster.db")

gse30521dat = getGEO('GSE30521')

gse30521raw= getGEOSuppFiles("GSE30521")

tarfile<- grep("\.tar$", rownames(gse30521raw), value = TRUE)

list.files("GSE30521")

untar("GSE30521/GSE30521_RAW.tar", exdir = "GSE30521/CEL")

list.files("GSE30521/CEL")

celfiles<- list.files("GSE30521/CEL", full = TRUE)

rawData<- read.celfiles(celfiles)

Error in read.celfile.header(x) :

Is GSE30521/CEL/GPL9793_gene_assignments.txt.gz really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats

anyone help me to solve this problem.

Answer 1

[PoGibas]

You are reading in NOT a cell file, that's the problem (R tells you this Is GSE30521/CEL/GPL9793_gene_assignments.txt.gz really a CEL file).

Try using pattern option in list.files so you would get only cell files. As now you are listing all files in directory.

list.files("GSE30521/CEL", full = TRUE)

Also, this line is useless.

tarfile<- grep("\.tar$", rownames(gse30521raw), value = TRUE)

[muhammadzubair777]

ARE U SAYING LIKE THIS

list.files("GSE30521", pattern="*.CEL")

[1] "GSM756911.CEL.gz" "GSM756912.CEL.gz" "GSM756913.CEL.gz" "GSM756914.CEL.gz" "GSM756915.CEL.gz" "GSM756916.CEL.gz" "GSM756917.CEL.gz" "GSM756918.CEL.gz" [9] "GSM756919.CEL.gz" "GSM756920.CEL.gz" "GSM756921.CEL.gz" "GSM756922.CEL.gz" "GSM756923.CEL.gz" "GSM756924.CEL.gz" "GSM756925.CEL.gz" "GSM756926.CEL.gz" [17] "GSM756927.CEL.gz" "GSM756928.CEL.gz" "GSM756929.CEL.gz" "GSM756930.CEL.gz" "GSM756931.CEL.gz" "GSM756932.CEL.gz" "GSM756933.CEL.gz"

rawData<- read.celfiles(celfiles)

Error: These do not exist: GSM756911.CEL.gz GSM756912.CEL.gz GSM756913.CEL.gz GSM756914.CEL.gz GSM756915.CEL.gz GSM756916.CEL.gz GSM756917.CEL.gz GSM756918.CEL.gz GSM756919.CEL.gz GSM756920.CEL.gz GSM756921.CEL.gz GSM756922.CEL.gz GSM756923.CEL.gz GSM756924.CEL.gz GSM756925.CEL.gz GSM756926.CEL.gz GSM756927.CEL.gz GSM756928.CEL.gz GSM756929.CEL.gz GSM756930.CEL.gz GSM756931.CEL.gz GSM756932.CEL.gz GSM756933.CEL.gz

[muhammadzubair777]

can you help me by modifying script?

[PoGibas]

read.celfiles assumes that files are in the current working directory, while in you case they are in GSE30521/CEL, i.e, you need full path to your files.